Try to think solely in terms of combat. Not PvE as a whole. Your argument is the same as someone saying that traders vs PvP ships are unbalanced, as they inherently should be. Mission runners are not combat ships. They can hold their own, and in many cases destroy every NPC threat. But that's combat against still vastly underpowered foes.
I think that's what most of us are talking about. One style of pure combat vs another. The optimal loadouts differ. It'd be nice if they didn't. We're not asking for normal missions to throw min-maxed NPCs with god skills at you. We're asking for them to exist in appropriate places so that a PvP player has PvE content to enjoy that won't end in hatemail or logging. :3
Ah, ok. Makes more sense.
In that case, pure PvP and PvE combat ships only differ in weapon choices, and FSD class/rating. There's very little else to separate them if the CMDR has engineered them to the maximum.
But, PvE only combat ships don't
need to be as "over engineered" as PvP, so the demand for "moar power!" tapers off for PvErs long before PvPers.
That's where the difference falls. Basically personal choice.
My combat (turned anti Thargoid) FDL is highly engineered, but is still no match for a "meta" PvP FDL.
But it also doesn't need to be, because NPC's and Thargoids aren't that big of a threat. (Ok, Thargoids can be, but I have the hitpoints and speed to escape if needed).
My FDL will likely never be fully engineered, because nothing I plan on doing with it requires it yet, so spending time doing so, is wasted time.
